Tax question: payroll error

This is the first time I have to file taxes by myself in Japan, so I’m a bit lost. I’m seeking advise how to deal with a speciffic issue, not tax advise (which I understand would be illegal)
I took some unpaid leave back in October, but the company messed up the salary calculation, and gave me waay more money than they should have. It took them awhile to figure it out, so in February, they took it back. However, for reasons that are too complex to list here, this year my total income will be significantly lower than last year. So the money they incorrectly gave me was taxed at let’s say 30% as per my last year tax bracket, but if that was done correctly, it would have been taxed at say 20% (because this year I’ll have much lower total income).
Of course payroll doesn’t give a shit, but the amount I lost is not pocket change.
If I would have done this the other way around, defer income to the next year to benefit from lower taxation, it would probably be criminal. But this happened, by no fault of mine, and I have to pay higher tax, for somebody’s screw-up.
Is there anything I can do, or I just have to suck it up?

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